A Modern Day Gene Genie Sir Richard Roberts on Rebase

Sir Richard Roberts
Nobel Prize winner and founder
of REBASE - Restriction Enzyme dataBASE - gives us a
snapshot of his work with restriction enzymes.

Can you provide an overview of the
aims and focus of the research activities
of REBASE?

The main aim of REBASE is to maintain
a comprehensive listing of all genes and
proteins associated with restriction modiﬁcation systems. Originally, this
was restricted to literature and personal
descriptions of new enzymes, but as
DNA sequencing became important, the
genes encoding known restriction system
components were included. Later, putative
restriction system components could be
identiﬁed by bioinformatics, so these too are
now an integral part of the database.

How did you ﬁrst come to be involved in
research around restriction enzymes?

In early 1972 I heard a lecture by Dan Nathans
at Harvard Medical School in which he
described the use of the ﬁrst Type II restriction
enzyme, Endonuclease R, to cleave SV40
DNA. This seemed to me to hold the key to
sequencing DNA and when I moved to Cold
Spring Harbor Laboratory later that year I
immediately began purifying this enzyme
and the few other restriction enzymes that
had been discovered in the interim. The
connection to NEB came later.

Roughly how many restriction enzymes
are known at this time? Do you expect this
number to keep growing?

More than 300 unique speciﬁcities have
been characterized, as well as several
hundred isoschizomers (enzymes that
recognize the same sequences as some of
those), but by examining the DNA of the
sequenced bacterial genomes we know that
many, many more exist. It is likely that many
thousands, perhaps hundreds of thousands,
are present in nature.

How would you describe the ethos of New
England Biolabs? In the 35 years since its
inception in the mid-1970s, would you say
the ethos has changed?

The original vision of Don Comb, the founder
of NEB, was to make money to support
research. I shared this vision completely and
so it was a perfect synergy for me to work
with him to make restriction enzymes the
ﬁ rst major commercial product of NEB. This
is still the overarching vision of the company.
The fact that Don is 83 and still an active
research scientist, together with the many
other researchers who contribute to the
success of the company, is what has allowed
us to maintain that original vision. Of course
the fact that we are still a private company
and not subject to the whims of shareholders,
who typically feel that research should stop to
increase their proﬁts, has been a major help

Relating to your Nobel Prize in 1993, for
your discovery with Phillip Sharp of ‘split
genes’: could you describe why it was so
signiﬁcant?

The signiﬁcance stems from the fact that
it completely changed our view of what
constituted a gene in eukaryotes (higher
organisms). It had repercussions throughout
eukaryotic biology and was of crucial
importance for interpreting the human genome
sequence, for example. It meant that all higher
organisms had an extra degree of complexity
in the way in which they used the information
encoded in their DNA. Even today we are still learning more about how split genes are
processed and ﬁnding additional complexities
in the regulation of the information present in
these split genes.

What did winning the Nobel Prize mean
to you as a scientist? Is it something you
aspired to or had imagined ever being
awarded?

I think every scientist dreams that perhaps
one day they might make a big discovery,
but few aspire to win a Nobel Prize. There
are very many discoveries being made all
the time and it is difﬁcult to know when
any one discovery becomes more important
than another. Luck plays a very signiﬁcant
role. As was famously said by Isaac Newton:
“If I see further than others it is because I
stand on the shoulders of giants”. This aptly
summarizes all research.

Clearly dissemination is at the core of
REBASE – how important do you consider
disseminating and sharing of research for
scientiﬁc progress?

Dissemination and sharing are key to all
research, but especially so when databases
have been compiled and the database
managers want as many people as possible
to see the results of their work. Much of the
dissemination of the contents of REBASE has
been in response to user requests over the
many years that I have been running it.

Splitting the building blocks of life

Since their discovery, restriction enzymes have proved key to unlocking the
doors of modern genomics and molecular biology. REBASE is a modern
tool to help scientists keep track of these wondrous proteins, while New
England Biolabs is an ethical company that supplies them to researchers.

Since DNA was ﬁrst discovered by Crick and
Watson in 1953, massive leaps have occurred in
the ﬁelds of genetics and molecular biology. One
such leap was in 1970, when Type II restriction
enzymes were ﬁrst isolated – a breakthrough
that opened new doors into our understanding
of how DNA is manipulated in nature, and led
the way for DNA sequencing and mapping, and
later recombinant DNA technology – techniques
which have since transformed modern medicine.

Type II restriction enzymes, or restriction
endonucleases, are found in bacteria, and have
the ability to recognise sequences in DNA, cutting
these with exquisite precision to produce speciﬁc
fragments (as opposed to Type I restriction
enzymes, which cut DNA randomly). In nature,
bacteria use these as a defense against invading
viruses (bacteriophages), whereby these enzymes
cleave foreign DNA in order to prevent invasion,
while simultaneously a methylase enzyme adds
a methyl group to the restriction site of its own
DNA, thus preventing it being attacked by its own
defenses. This system is known as restriction-modiﬁcation. In 1971, Danna and Nathans were
the ﬁrst to realize that the small fragments
produced by restriction enzymes could be used
to map DNA molecules and hence the cleavage
sites could be used as landmarks with which to
track genetic traits

THE ROOTS OF REBASE

One man has taken the work of Danna and
Nathans and pushed it to new heights. Sir
Richard Roberts, the winner of the 1993 Nobel
Prize in Physiology or Medicine (with Phillip
Sharp) for his groundbreaking discovery of split
genes. Inspired by a lecture given by Nathans
himself in 1972, Roberts was also instrumental
in isolating most of the world’s ﬁrst known
restriction enzymes. As a pioneer in this ﬁeld,
requests for lists of these enzymes came ﬂooding
in, eventually leading to the formation of a
database named REBASE (Restriction Enzyme
dataBASE), containing a listing of not only all the
restriction-modiﬁcation enzyme systems, but
also the genes encoding these.

THE REBASE WEBSITE HOMEPAGE

REBASE has since evolved into a web-based
format (rebase.neb.com) with a searchable
interface and a plethora of invaluable information.
New developments have meant that categories
are added to the database as appropriate. An
example of this occurred when the Haemophilus
inﬂuenza genome was sequenced in 1995, leading
to the inclusion of putative restriction system
components. Technological advances have led
to users being able to BLAST (use a Basic Local
Alignment Search Tool) new genome sequences
to ﬁ nd restriction system components, and also help to determine recognition sequences
of new restriction enzymes. Other tools include
NEBcutter, which produces lists of user-submitted DNA sequences and maps of cutting
sites. In addition, monthly lists of known enzymes
and details of their commercial availability are
sent out to researchers and interested parties.
The formation of such an interactive and
comprehensive database requires a variety of
means: “REBASE depends on both biochemical
and bioinformatic methods to produce its
contents,” Roberts explains.

NEW ENGLAND BIOLABS

While Roberts is a pioneer in his ﬁeld, and also at
the forefront in the dissemination of everything
currently known about restriction enzymes, he
also plays a major role in the commercial side of
his and others’ discoveries. He is currently Chief
Scientiﬁc Ofﬁcer of New England Biolabs (NEB),
a company founded by Don Comb, whom he
ﬁrst met in the 1970s. At that time, Comb had
set up a small laboratory with his wife and a
technician, and was planning to start selling the
ﬁ rst restriction enzyme. With a large collection
of his own, Roberts soon joined forces with Comb
as their chief consultant. The rest, as they say,
is history, as NEB was the ﬁrst company to sell
restriction enzymes and other research reagents
that have since driven the biotechnology industry.

As the leader in high quality research products,
and the largest supplier of restriction enzymes
in the world, one might expect NEB to be run
on traditional, proﬁt-driven corporate values.
However, even in such a ﬁercely competitive and
often cut-throat world, the company has managed
to remain not only successful, but has been able
to do so without compromising their original
principles: to create revenue that helps fund
research. It is still a private company that believes
in sustainable, ecological practices. Comb remains
actively involved in research, but has handed over
the day-to-day running of the company to James
Ellard. Roberts is well aware of the road ahead for
such an ethical operation: “The challenge for the
future will be to maintain the company ethos and
make sure that we continue to provide top quality
reagents for research,” he muses.

The ethical work of NEB is also mirrored in the
NEB Foundation, which was set up by Comb in
1982. It is an independent, private venture which
supports grass roots organisations that encourage
conservation of biological and cultural diversity,
maintain terrestrial and marine ecosystems, and
support local communities, as well as promoting
arts projects.

INSPIRATION

As an eminent scientist and Knight of the Realm,
Roberts is quick to acknowledge those who
inspired him to follow the path that he ended
up taking. From his headmaster at primary
school, Mr Broakes, who engendered his love
of mathematics, to Professor David Ollis, who
introduced him to the joys of organic chemistry
by challenging his then potentially brilliant young
mind. He is also thankful to author John Kendrew
for bringing to life the world of molecular biology
after reading The Thread of Life, while his postdoctoral advisor, Jack Strominger, mentored
and encouraged him to follow his dreams.
Furthermore, he is grateful to Uttam RajBhandary
at MIT for teaching him about tRNAs and research
techniques. Ever humble, he puts across his views
on what would be the pinnacle of any scientist’s
career – the Nobel Prize: “Phil and I were lucky
to be working in the right area, at the right time,
and to make the critical observations that led to
what turned out to be a very important discovery
because it completely changed the way biologists
thought about genes”.

INTELLIGENCE

REBASE: THE RESTRICTION ENZYME DATABASE

Objectives

This project concerns the maintenance and
distribution of a cohesive and comprehensive
database of information about restriction
endonucleases and their associated
methyltransferases. Key components of the
database are information about the methyl
sensitivity of restriction endonucleases and
a comprehensive analysis of the restriction
enzymes present in the sequenced microbial
genomes. REBASE is a unique resource for the
practice of biotechnology and its contents are
used directly or indirectly by many sections of
the research healthcare community. REBASE
serves as the master database used by both
academics and commercial companies
to ﬁ nd out which restriction enzymes are
commercially available.

Funding

National Library of Medicine (LM04971)

Key Collaborators

Dana Macelis
Karen Otto
Tamas Vincze
Janos Posfai

Contact

Dr. Roberts was educated in chemistry at
Shefﬁeld University and molecular biology at
Harvard University. He worked for 20 years
at Cold Spring Harbor Laboratory where his
group discovered RNA splicing for which he
was awarded the Nobel Prize in 1993. In 1992
he moved to New England Biolabs as Director
of eukaryotic research before becoming
Chief Scientiﬁc ofﬁcer in 2005. He has had
a long-standing interest in bioinformatics,
which most recently had been applied to his
research on restriction enzymes.